[gmx-users] Re: Mdrun interrupted using a triclinc box

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Oct 7 11:00:35 CEST 2005

Xie Yinghong,

There's no such thing as a box in your simulation. Check the manual
and the user list for 'periodic boundary conditions'. In your
simulation you have an infinite system, which consists of a base,
which is replicated along the lattice vectors, so to speak. The box
you defined for your system is triclinic, but can also be represented
as a perfect regular hexagonal prism.

trjconv -pbc whole keeps your molecules together. If you find it in
seperate locations, either you simulated a multimer and you'd be
better off using -pbc cluster, or you're system exploded due to errors
in the starting structure or topology. The latter would be a cause for
a simulation to crash. However, nothing of what you stated can give us
any clue to why you're simulation stopped. Did grompp give any
warnings during processing? Have you checked the energies during the
simulation and the presence of LINCS warnings?



On 10/7/05, Yinghong <xieyh at hkusua.hku.hk> wrote:
> Dear users:
> In my system, I chose a triclinc box (monoclinic cell) as my periodic
> boundary condition, which is defined as follows:
> editconf -f *.pdb -o -bt tric -box 5 5 10 -angles 90 90 120 -c
> genbox -cp out -cs -p topol -o b4em
> grompp -v -f em -c b4em -p topol -o box
> trjconv -f b4em -s box -o b4em2.gro -ur tric -pbc inbox
> If I used "-pbc inbox", my simulated molecule would be broken. And, if "-pbc
> whole" was adapted, the molecule could be kept intact, but Gromacs told me
> that has no effect for unit cell representation.
> In my simulations, I empolyed "-pbc whole" in order to keep molecule intact,
> but after ~200ps simulation, mdrun is interrupted, and the initial intact
> molecule is also broken at this moment.
> So, Could you tell me that the way I defined a triclinc box (not hexagonal
> box) is right?
> Which option should I choose in "trjconv" for -ur and -pbc?
> What made my simulation stopped?
> Because this is my first time using triclinc box, many things are very
> strange for me.
> Any help is appreciated.
> Xie Yinghong
> Hong Kong University


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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